24 papers · ranked by Valyu relevance
Sarthak Mittal, Yoshua Bengio, Guillaume Lajoie
Inspired from human cognition, machine learning systems are gradually revealing advantages of sparser and more modular architectures. Recent work demonstrates that not only do some modular architectures generalize well, but they also lead to better out-of-distribution generalization, scaling properties, learning speed…
Alexander Rittner, Karthik S. Paithankar, David Drexler, Aaron Himmler + 1 more
Modularity is an aspect of a decomposable system with a coordinating authority that acts as a glue which holds the loosely held components. These multi-component entities (“modules”) facilitate rewiring into different designs allowing for change. Such modular character is a fundamental property of many biological…
Babak Heydari, Mohsen Mosleh, Kia Dalili
This paper introduces a conceptual, yet quantifiable, architecture framework by extending the notion of system modularity in its broadest sense. Acknowledging that modularity is not a binary feature and comes in various types and levels, the proposed framework introduces higher levels of modularity that naturally…
Saúl Huitzil, Cristián Huepe
Modularity, the structuring of systems into discrete, interconnected units, is a fundamental organizing principle in biology across multiple scales. Recent progress in understanding the role of modularity as an evolutionary mechanism and a key driver of biological complexity has highlighted its importance in shaping…
Lars A. L. Janssen, R.H.B. Fey, Bart Besselink, Nathan van de Wouw
Specifications Guaranteeing System Dynamics Specifications Authors: ['Lars A. L. Janssen' 'R.H.B. Fey' 'Bart Besselink' 'Nathan van de Wouw'] Complex mechatronic systems are typically composed of interconnected modules, often developed by independent teams. This development process challenges the verification of system…
Michael Pan, Peter J. Gawthrop, Joseph Cursons, Edmund J. Crampin
It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling problems to be broken up into more manageable pieces. To this end, both modelling and software frameworks are required to enable modular modelling. While there has been consistent progress in the…
Maxwell L. Neal, Michael T. Cooling, Lucian P. Smith, Christopher T. Thompson + 5 more
Biological researchers increasingly rely on computational models to integrate biological systems knowledge, test hypotheses, and forecast system behavior. The expanding size of these models requires solutions for managing their complexity. Modularity, a time-tested design principle for managing complexity, can be…
Michael Pan, Peter J. Gawthrop, Joseph Cursons, Edmund J. Crampin + 1 more
'Anders Wallqvist'] It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling problems to be broken up into more manageable pieces. To this end, both modelling and software frameworks are required to enable modular modelling. While there has been…
Mark Sh. Levin
The paper briefly describes a basic set of special combinatorial engineering frameworks for solving complex problems in the field of hierarchical modular systems. The frameworks consist of combinatorial problems (and corresponding models), which are interconnected/linked (e.g., by preference relation). Mainly…
Claus Kadelka, Matthew Wheeler, Alan Veliz-Cuba, David Murrugarra + 1 more
This paper addresses two topics in systems biology, the hypothesis that biological systems are modular and the problem of relating structure and function of biological systems. The focus here is on gene regulatory networks, represented by Boolean network models, a commonly used tool. Most of the research on gene…
Claus Kadelka, Matthew Wheeler, Alan Veliz-Cuba, David Murrugarra + 1 more
This paper addresses two topics in systems biology, the hypothesis that biological systems are modular and the problem of relating structure and function of biological systems. The focus here is on gene regulatory networks, represented by Boolean network models, a commonly used tool. Most of the research on gene…
Tihana Galinac Grbac
This is part I of the follow-up lecture notes of the lectures given by the authors at the Three "CO" (Composability, Comprehensibility, Correctness) Winter School held in Koˇsice, Slovakia, in January 2018, and Summer School held in Budapest, Hungary, in June 2019. In this part we explain the role of functional…
Sergio Garcia, Cong T. Trinh
Living cells optimize their fitness against constantly changing environments to survive. Goal attainment optimization is a mathematical framework to describe the simultaneous optimization of multiple conflicting objectives that must all reach a performance above a threshold or goal. In this study, we applied goal…
Brenden K Petersen, Glen EP Ropella, C Anthony Hunt
Background Currently, most biomedical models exist in isolation. It is often difficult to reuse or integrate models or their components, in part because they are not modular. Modular components allow the modeler to think more deeply about the role of the model and to more completely address a modeling project’s…
Christopher Schölzel, Valeria Blesius, Gernot Ernst, Andreas Dominik
Reproducible, understandable models that can be reused and combined to true multi-scale systems are required to solve the present and future challenges of systems biology. However, many mathematical models are still built for a single purpose and reusing them in a different context can be challenging due to an…
Anna Matuszyńska, Oliver Ebenhöh, Matias D. Zurbriggen, Daniel C. Ducat + 1 more
Synthetic biology designs and constructs new biological parts, devices and systems with predetermined functionalities. With the unlimited ability to synthesise any DNA and RNA and transfer it to almost any organism, we are at the dawn of a new era in which biology is being recreated in ways never before possible. It…
Johannes Jaeger, Nick Monk
Modularity is an essential feature of any adaptive complex system. Phenotypic traits are modules in the sense that they have a distinguishable structure or function, which can vary (quasi-)independently from its context. Since all phenotypic traits are the product of some underlying regulatory dynamics, the generative…
Francesco Benso, Carlo Chiorri, Eleonora Ardu, Paola Venuti + 1 more
'Angela Pasqualotto'] The concept of modularity in neuropsychology remains a topic of significant debate, especially when considering complex, non-innate, hyper-learned, and adaptable modular systems. This paper critically examines the evolution of cognitive modularity, addressing the challenges of integrating…
Alejandro Santana-Bonilla, Raquel Lopez-Rios De Castro, Peike Sun, Robert Ziolek + 1 more
Machine learning methods offer the opportunity to design new functional materials on an unprecedented scale however building the large, diverse databases of molecules on which to train such methods remains a daunting task. Automated computational chemistry modelling workflows are therefore becoming essential tools in…
Shuaijian Dai, Yage Zhang, Weichuan Yu, Ning Li
Proteins are organized into modules by both functions and physical interactions within compartments of an eukaryotic cell. The in vivo chemical crosslinking mass spectrometry (XL-MS) data collected from organelles, the whole cells and tissues are able to provide unique information about both protein-protein interaction…
Authors not listed
Rapid and robust simulation of chemical processes is critical to conduct process design, optimization, techno-economic analysis, and sustainability analysis. Yet, efficiently solving simulation models remains a challenge due to the highly coupled and nonlinear nature of the underlying algebraic equations that capture…
Pablo Quijano Velasco, Kedar Hippalgaonkar, Balamurugan Ramalingam
The discovery of optimal conditions of chemical reactions is a labor-intensive, time-consuming task that requires exploring a high-dimensional parametric space. Historically the optimization of chemical reactions has been performed by manual experimentation guided by human intuition and Design of Experiments where one…
Fatemeh Hashemniya, Benoı̂t Caillaud, Erik Frisk, Mattias Krysander + 1 more
'Mathias Malandain'] Abstract: Multi-mode systems can operate in different modes, leading to large numbers of different dynamics. Consequently, applying traditional structural diagnostics to such systems is often untractable. To address this challenge, we present a multi-mode diagnostics algorithm that relies on a…
Alexandra Hindle, Krzysztof Baj, Jonathan Iggo, Daniel Cox + 3 more
Bridged amides and anilines display interesting properties owing to perturbation of conjugation of the nitrogen lone-pair with the adjacent π-system. A convergent approach to diazabicyclic scaffolds which contain either twisted amides or anilines is described, based on the photocatalysed hydroamination of cyclic…